Remove the build dependency

.devcontainer/Dockerfile

@@ -1,74 +1,45 @@
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 ENV TZ=Europe/Berlin
-ENV PYENV_ROOT="/opt/.pyenv"
-ENV PATH="$PYENV_ROOT/bin:$PATH"
-ENV PATH="/opt/.pyenv/versions/3.9.1/bin/:$PATH"
 ENV DISPLAY=:1
 ENV XDG_RUNTIME_DIR=/tmp/runtime-root
 
-RUN unset Qt5_DIR ParaView_DIR ROOT_INCLUDE_PATH CMAKE_PREFIX_PATH PYENV_ROOT BDMSYS CC CXX
-
-RUN apt-get -y update && \
-    apt-get -y install apt-utils software-properties-common python python3 git curl make gcc g++ wget \
-    wamerican libffi-dev libncurses5-dev zlib1g zlib1g-dev bzip2 aptitude libreadline-dev libssl-dev \
-    libsqlite3-dev openmpi-bin libopenmpi-dev libxkbcommon-x11-dev bsdmainutils clang clang-format \
-    clang-tidy doxygen graphviz libxml2-dev llvm-7 llvm-7-dev llvm-7-runtime valgrind libgsl-dev \
-    freeglut3-dev libbz2-dev libnuma-dev libomp5 libomp-dev libpthread-stubs0-dev zlib1g-dev \
-    libffi-dev liblzma-dev libreadline-dev libsqlite3-dev libssl-dev python-openssl tk-dev xz-utils \
-    zlib1g-dev sudo libblas-dev liblapack-dev nano locales locales-all ninja-build python3-pip \
-    freeglut3-dev valgrind xvfb libtbb-dev \
-    x11vnc fluxbox websockify \
-    novnc dbus-x11 x11-utils x11-xserver-utils xterm && \
-    dpkg-reconfigure locales && locale-gen && \
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+      ca-certificates cmake curl fluxbox g++ gcc git libblas-dev libboost-dev \
+      libdouble-conversion-dev liblapack-dev libnuma-dev libomp-dev \
+      libopenmpi-dev libutfcpp-dev ninja-build novnc openmpi-bin paraview \
+      paraview-dev python3 sudo websockify wget x11-utils x11vnc \
+      x11-xserver-utils xterm xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
-RUN curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash && \
-    eval "$(pyenv init --path)" && \
-    eval "$(pyenv init -)" && \
-    PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1 && \
-    pyenv global 3.9.1 && \
-    pyenv shell 3.9.1
-
-RUN wget https://bootstrap.pypa.io/get-pip.py && \
-    python3 get-pip.py && \
-    python3 -m pip install -U pip && \
-    python3 -m pip install numpy
-
-RUN pip install 'cmake<4'
-
 RUN git config --system user.name "Test User" && \
     git config --system user.email user@test.com
 
-RUN export BDM_BRANCH="master" && \
-    git clone https://github.com/BioDynaMo/biodynamo.git && \
-    cd biodynamo && \
-    git checkout $BDM_BRANCH && \
-    git rev-parse HEAD > /commit_hash.txt && \
-    cat /commit_hash.txt && \
-    mkdir build && \
-    cd build && \
-    cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -Dtest=OFF -Dgtest=OFF -Dbenchmark=OFF \
-      -Dparaview=ON -DCMAKE_POLICY_DEFAULT_CMP0048=NEW -DCMAKE_POLICY_DEFAULT_CMP0054=NEW \
-      -DCMAKE_POLICY_DEFAULT_CMP0056=NEW -DCMAKE_POLICY_DEFAULT_CMP0066=NEW \
-      -DCMAKE_POLICY_DEFAULT_CMP0067=NEW -DCMAKE_POLICY_DEFAULT_CMP0074=NEW .. && \
-    ninja -j $(($(nproc) - 1))
+RUN git clone --depth 1 --branch master https://github.com/BioDynaMo/biodynamo.git /biodynamo && \
+    cmake -S /biodynamo -B /biodynamo/build -G Ninja \
+      -Dbenchmark=OFF \
+      -Dcuda=OFF \
+      -Dlibgit2=OFF \
+      -Dopencl=OFF \
+      -Dparaview=ON \
+      -Dsbml=OFF \
+      -Dtest=OFF \
+      -Dvalgrind=OFF \
+      -DCMAKE_BUILD_TYPE=Release && \
+    cmake --build /biodynamo/build --parallel
 
 RUN useradd -m -s /bin/bash codespace && \
-    echo "codespace ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
-
-RUN mkdir -p /tmp/runtime-root && chmod 700 /tmp/runtime-root
+    echo "codespace ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers && \
+    mkdir -p /tmp/runtime-root /opt/scripts && \
+    chmod 700 /tmp/runtime-root
 
 RUN echo 'source /biodynamo/build/bin/thisbdm.sh 2>/dev/null' >> /etc/bash.bashrc
 
 COPY novnc-index.html /usr/share/novnc/index.html
-
-RUN mkdir -p /opt/scripts
-COPY start-vnc.sh /opt/scripts/start-vnc.sh
-RUN chmod +x /opt/scripts/start-vnc.sh
-COPY demo-picker.sh /opt/scripts/demo-picker.sh
-RUN chmod +x /opt/scripts/demo-picker.sh
+COPY start-vnc.sh demo-picker.sh /opt/scripts/
+RUN chmod +x /opt/scripts/start-vnc.sh /opt/scripts/demo-picker.sh
 
 COPY paraview-wrapper.sh /usr/local/bin/paraview
 RUN chmod +x /usr/local/bin/paraview

.devcontainer/paraview-wrapper.sh

@@ -6,6 +6,4 @@ echo "Switch to the port 6080 browser tab to see the GUI."
 echo "If not open yet: Ports tab -> 6080 -> Open in Browser"
 echo ""
 
-# Find the real paraview binary (skip this wrapper)
-REAL_PARAVIEW=$(which -a paraview | grep -v /usr/local/bin | head -1)
-exec "$REAL_PARAVIEW" "$@"
+exec /usr/bin/paraview "$@"

.github/workflows/ci.yml

@@ -0,0 +1,173 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: '0 3 * * *'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  linux:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04, ubuntu-24.04]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libblas-dev libboost-dev liblapack-dev libnuma-dev libomp-dev \
+            libopenmpi-dev ninja-build
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -Dbenchmark=OFF \
+            -Dcuda=OFF \
+            -Dlibgit2=OFF \
+            -Dopencl=OFF \
+            -Dparaview=OFF \
+            -Dsbml=OFF \
+            -Dvalgrind=OFF \
+            -DCMAKE_BUILD_TYPE=Release
+      - name: Build
+        run: cmake --build build --parallel
+      - name: Test
+        run: cmake --build build --target run-unit-tests
+
+  macos:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-14, macos-15]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: brew install boost cmake libomp ninja open-mpi
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -Dbenchmark=OFF \
+            -Dcuda=OFF \
+            -Dlibgit2=OFF \
+            -Dopencl=OFF \
+            -Dparaview=OFF \
+            -Dsbml=OFF \
+            -Dvalgrind=OFF \
+            -DCMAKE_BUILD_TYPE=Release
+      - name: Build
+        run: cmake --build build --parallel
+      - name: Test
+        run: cmake --build build --target run-unit-tests
+
+  paraview:
+    runs-on: ubuntu-24.04
+    env:
+      QT_QPA_PLATFORM: offscreen
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libblas-dev libboost-dev liblapack-dev libomp-dev \
+            libdouble-conversion-dev libopenmpi-dev libutfcpp-dev ninja-build \
+            paraview paraview-dev
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -Dbenchmark=OFF \
+            -Dcuda=OFF \
+            -Dlibgit2=OFF \
+            -Dnuma=OFF \
+            -Dopencl=OFF \
+            -Dparaview=ON \
+            -Dsbml=OFF \
+            -Dvalgrind=OFF \
+            -DCMAKE_BUILD_TYPE=Release
+      - name: Build
+        run: cmake --build build --parallel
+      - name: Test
+        run: cmake --build build --target run-unit-tests
+
+  sanitizers:
+    runs-on: ubuntu-24.04
+    env:
+      ASAN_OPTIONS: detect_leaks=1:halt_on_error=1
+      UBSAN_OPTIONS: halt_on_error=1:print_stacktrace=1
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libblas-dev libboost-dev liblapack-dev libomp-dev \
+            libopenmpi-dev ninja-build
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -Dbenchmark=OFF \
+            -Dcuda=OFF \
+            -Dlibgit2=OFF \
+            -Dnuma=OFF \
+            -Dopencl=OFF \
+            -Dparaview=OFF \
+            -Dsbml=OFF \
+            -Dvalgrind=OFF \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DCMAKE_C_FLAGS='-fsanitize=address,undefined -fno-omit-frame-pointer' \
+            -DCMAKE_CXX_FLAGS='-fsanitize=address,undefined -fno-omit-frame-pointer' \
+            -DCMAKE_EXE_LINKER_FLAGS='-fsanitize=address,undefined' \
+            -DCMAKE_SHARED_LINKER_FLAGS='-fsanitize=address,undefined'
+      - name: Build
+        run: cmake --build build --parallel
+      - name: Test
+        run: cmake --build build --target run-unit-tests
+
+  singularity:
+    runs-on: ubuntu-24.04
+    container:
+      image: quay.io/singularity/singularity:v3.9.0
+      options: --privileged --workdir /data
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure fakeroot
+        run: |
+          echo root:100000:65536 >> /etc/subuid
+          echo root:100000:65536 >> /etc/subgid
+      - name: Build image
+        run: singularity build --fakeroot biodynamo.sif Singularity
+      - name: Run demo
+        run: |
+          singularity exec --cleanenv biodynamo.sif bash -lc '
+            source /biodynamo/build/bin/thisbdm.sh
+            cd "$(mktemp -d)"
+            bdm demo tumor_concept
+            cd tumor_concept
+            bdm run'
+
+  repository:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y clang-format
+      - name: Check formatting
+        run: |
+          ./util/housekeeping/run-clang-format.sh \
+            "$(pwd)" clang-format 0 $(./util/housekeeping/get-all-src-files.sh .)
+      - name: Check copyright
+        run: |
+          ./util/housekeeping/check-copyright.sh \
+            util/housekeeping/copyright_cpp.txt \
+            $(./util/housekeeping/get-all-src-files.sh .)